Jonathan King

How are mask records generated?

1

Hi Mohammed, Thanks for this great resource and congratulations on its recent publication. I'm curious - can you share your method for generating mask records? Best, Jonathan

Does ProDy support identifying missing residues from .cif files?

8

I need to be able to parse .cif files so that I have access to the complete protein chain sequence along with annotations for which residues are unobserved or 0...

I've found that I'm unable to load the provided openfold model parameters when using `--resume_model_weights_only=True` in `train_openfold.py` . An error arises because the keys corresponding the model parameters are prefixed...

Should train_chain_data_cache_path be a required argument?

2

Although the current argparse parser allows the user to not pass a value for `train_chain_data_cache_path`, the current implementation of `data_modules.OpenFoldDataset` (specifically the inner function, `looped_samples`) assumes that the cache object...

## Background First, I want to thank everyone that has contributed to OpenFold’s development, as well as the development of RODA. I really value the hard work that has gone...

Allow initialization from topology, positions, and sequence.

1

This allows the user to fix an object/protein structure already loaded by OpenMM. I have used this in my research so I can fix an already parsed protein structure instead...